Second-order discontinuous Galerkin flood model: comparison with industry-standard finite volume models

Finite volume (FV) numerical solvers of the two-dimensional shallow water equations are core to industry-standard flood models. The second-order Discontinuous Galerkin (DG) alternative is well-known to perform better than first- and second-order FV to capture sharp flow fronts and converge faster at coarser resolutions, but DG2 models typically rely on local slope limiting to selectively damp numerical oscillations in the vicinity of shock waves. Yet flood inundation events are smooth and gradually-varying, and shock waves play only a minor role in flood inundation modelling. Therefore, this paper investigates two DG2 variants - with and without local slope limiting - to identify the simplest and most efficient DG2 configuration suitable for flood inundation modelling. The predictive capabilities of the DG2 variants are analysed for a synthetic test case involving advancing and receding waves representative of flood-like flow. The DG2 variants are then benchmarked against industry-standard FV models over six UK Environment Agency scenarios. Results indicate that the DG2 variant without local slope limiting closely reproduces solutions of the commercial models at twice as coarse a spatial resolution, and removing the slope limiter can halve model runtime. Results also indicate that DG2 can capture more accurate hydrographs incorporating small-scale transients over long-range simulations, even when hydrographs are measured far away from the flooding source. Accompanying details of software and data accessibility are provided

Where does Flavour Mixing come from?

We argue that flavour mixing, both in the quark and charged lepton sector, is basically determined by the lightest family mass generation mechanism. So, in the chiral symmetry limit when the up and down quark masses vanish, all the quark mixing angles vanish. This mechanism is not dependent on the number of quark-lepton families nor on any ``vertical'' symmetry structure, unifying quarks and leptons inside a family as in Grand Unified Theories. Together with a hypothesis of maximal CP violation, the model leads to a completely predictive ansatz for all the CKM matrix elements in terms of the quark masses. Some implications for neutrino masses and oscillations are briefly discussed.Comment: 13 page LaTeX file, minor changes in fourth paragraph of Conclusion and in Reference

Size dependent symmetry breaking in models for morphogenesis

A general property of dynamical systems is the appearance of spatial and temporal patterns due to a change of stability of a homogeneous steady state. Such spontaneous symmetry breaking is observed very frequently in all kinds of real systems, including the development of shape in living organisms. Many nonlinear dynamical systems present a wide variety of patterns with different shapes and symmetries. This fact restricts the applicability of these models to morphogenesis, since one often finds a surprisingly small variation in the shapes of living organisms. For instance, all individuals in the Phylum Echinodermata share a persistent radial fivefold symmetry. In this paper, we investigate in detail the symmetry-breaking properties of a Turing reaction–diffusion system confined in a small disk in two dimensions. It is shown that the symmetry of the resulting pattern depends only on the size of the disk, regardless of the boundary conditions and of the differences in the parameters that differentiate the interior of the domain from the outer space. This study suggests that additional regulatory mechanisms to control the size of the system are of crucial importance in morphogenesis

Interactions between Simulant Vitrified Nuclear Wastes and high pH solutions: A Natural Analogue Approach

This study details the characterization of a glass sample exposed to hyperalkaline water and calcium-rich sediment for an extended time period (estimated as 2-70 years) at a lime (CaO) waste site in the UK. We introduce this site, known as Peak Dale, in reference to its use as a natural analogue for nuclear waste glass dissolution in the high pH environment of a cementitious engineered barrier of a geological disposal facility. In particular, a preliminary assessment of alteration layer chemistry and morphology is described and the initiation of a long-term durability assessment is outlined

Heterogeneous glycosylation and methylation of the Aeromonas caviae flagellin

Bacterial swimming is mediated by the rotation of a flagellar filament. Many bacteria are now known to be able to O-glycosylate their flagellins, the proteins that make up the flagellar filament. For bacteria that use nonulosonic acid sugars such as pseudaminic acid, this glycosylation process is essential for the formation of a functional flagellum. However, the specific role of glycosylation remains elusive. Aeromonas caviae is a model for this process as it has a genetically simple glycosylation system. Here, we investigated the localization of the glycans on the A. caviae flagellum filament. Using mass spectrometry it was revealed that pseudaminic acid O-glycosylation was heterogeneous with no serine or threonine sites that were constantly glycosylated. Site-directed mutagenesis of particular glycosylation sites in most cases resulted in strains that had reduced motility and produced less detectable flagellin on Western blots. For flagellin O-linked glycosylation, there is no known consensus sequence, although hydrophobic amino acids have been suggested to play a role. We, therefore, performed site-directed mutagenesis of isoleucine or leucine residues flanking the sites of glycosylation and demonstrated a reduction in motility and the amount of flagellin present in the cells, indicating a role for these hydrophobic amino acids in the flagellin glycosylation process

The Aeromonas caviae AHA0618 gene modulates cell length and influences swimming and swarming motility

Aeromonas caviae is motile via a polar flagellum in liquid culture, with a lateral flagella system used for swarming on solid surfaces. The polar flagellum also has a role in cellular adherence and biofilm formation. The two subunits of the polar flagellum, FlaA and FlaB, are posttranslationally modified by O-linked glycosylation with pseudaminic acid on 6–8 serine and threonine residues within the central region of these proteins. This modification is essential for the formation of the flagellum. Aeromonas caviae possesses the simplest set of genes required for bacterial glycosylation currently known, with the putative glycosyltransferase, Maf1, being described recently. Here, we investigated the role of the AHA0618 gene, which shares homology (37% at the amino acid level) with the central region of a putative deglycosylation enzyme (HP0518) from the human pathogen Helicobacter pylori, which also glycosylates its flagellin and is proposed to be part of a flagellin deglycosylation pathway. Phenotypic analysis of an AHA0618 A. caviae mutant revealed increased swimming and swarming motility compared to the wild-type strain but without any detectable effects on the glycosylation status of the polar flagellins when analyzed by western blot analysis or mass spectroscopy. Bioinformatic analysis of the protein AHA0618, demonstrated homology to a family of l,d-transpeptidases involved in cell wall biology and peptidoglycan cross-linking (YkuD-like). Scanning electron microscopy (SEM) and fluorescence microscopy analysis of the wild-type and AHA0618-mutant A. caviae strains revealed the mutant to be subtly but significantly shorter than wild-type cells; a phenomenon that could be recovered when either AHA0618 or H. pylori HP0518 were introduced. We can therefore conclude that AHA0618 does not affect A. caviae behavior by altering polar flagellin glycosylation levels but is likely to have a role in peptidoglycan processing at the bacterial cell wall, consequently altering cell length and hence influencing motility

Consistent Anisotropic Repulsions for Simple Molecules

We extract atom-atom potentials from the effective spherical potentials that suc cessfully model Hugoniot experiments on molecular fluids, e.g., $O_2$ and $N_2$. In the case of $O_2$ the resulting potentials compare very well with the atom-atom potentials used in studies of solid-state propertie s, while for $N_2$ they are considerably softer at short distances. Ground state (T=0K) and room temperatu re calculations performed with the new $N-N$ potential resolve the previous discrepancy between experimental and theoretical results.Comment: RevTeX, 5 figure

Edge effects in a frustrated Josephson junction array with modulated couplings

A square array of Josephson junctions with modulated strength in a magnetic field with half a flux quantum per plaquette is studied by analytic arguments and dynamical simulations. The modulation is such that alternate columns of junctions are of different strength to the rest. Previous work has shown that this system undergoes an XY followed by an Ising-like vortex lattice disordering transition at a lower temperature. We argue that resistance measurements are a possible probe of the vortex lattice disordering transition as the linear resistance $R_{L}(T)\sim A(T)/L$ with $A(T) \propto (T-T_{cI})$ at intermediate temperatures $T_{cXY}>T>T_{cI}$ due to dissipation at the array edges for a particular geometry and vanishes for other geometries. Extensive dynamical simulations are performed which support the qualitative physical arguments.Comment: 8 pages with figs, RevTeX, to appear in Phys. Rev.

Minimal Mixing of Quarks and Leptons in the SU(3) Theory of Flavour

We argue that flavour mixing, both in the quark and lepton sector, follows the minimal mixing pattern, according to which the whole of this mixing is basically determined by the physical mass generation for the first family of fermions. So, in the chiral symmetry limit when the masses of the lightest ($u$ and $d$) quarks vanish, all the quark mixing angles vanish. This minimal pattern is shown to fit extremely well the already established CKM matrix elements and to give fairly distinctive predictions for the as yet poorly known ones. Remarkably, together with generically small quark mixing, it also leads to large neutrino mixing, provided that neutrino masses appear through the ordinary ``see-saw'' mechanism. It is natural to think that this minimal flavour mixing pattern presupposes some underlying family symmetry, treating families of quarks and leptons in a special way. Indeed, we have found a local chiral $SU(3)_{F}$ family symmetry model which leads, through its dominant symmetry breaking vacuum configuration, to a natural realization of the proposed minimal mechanism. It can also naturally generate the quark and lepton mass hierarchies. Furthermore spontaneous CP violation is possible, leading to a maximal CP violating phase $\delta =\frac{\pi}{2}$, in the framework of the MSSM extended by a high-scale $SU(3)_{F}$ chiral family symmetry.Comment: 52 pages, LaTex, no figures; some typos corrected; journal versio